Contacts of the helix formed by residues 462 - 473 (chain D) in PDB entry 1CCW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 462 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431D LEU* 3.7 13.2 - - - +
459D ARG* 5.5 1.9 + - - -
460D ASP* 3.4 10.9 + - - -
461D VAL* 1.3 81.1 - - - +
463D PHE* 1.3 64.2 + - - +
464D GLN* 3.3 19.6 + - - +
465D MET* 3.0 25.2 + - - +
466D VAL* 3.3 11.1 + - - +
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Residues in contact with PHE 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS* 6.2 3.8 - - + -
22C ILE* 5.3 6.1 - - + -
25C HIS* 4.0 24.7 - + + -
408D PHE* 5.1 12.8 - + - -
419D MET* 3.7 36.4 - - + -
431D LEU* 4.2 2.2 - - - +
462D SER* 1.3 74.9 - - - +
464D GLN* 1.3 60.7 + - - +
466D VAL* 3.0 25.1 + - + +
467D ILE* 3.0 48.9 + - + +
470D ILE* 5.9 1.3 - - + -
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Residues in contact with GLN 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C HIS* 4.9 5.2 + - - -
459D ARG* 4.0 17.9 - - - +
462D SER* 3.2 12.9 + - - +
463D PHE* 1.3 77.7 - - - +
465D MET* 1.3 57.3 + - - +
467D ILE* 3.2 29.7 + - - +
468D ASP* 2.9 48.8 + - - +
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Residues in contact with MET 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D VAL* 3.7 10.5 - - + -
453D ARG* 3.7 37.9 + - + +
454D ALA* 4.4 3.1 - - - -
457D GLU* 3.6 17.3 - - - +
459D ARG* 3.6 39.3 - - + +
460D ASP 3.8 7.4 - - - +
461D VAL* 3.7 42.2 - - + -
462D SER* 3.0 16.2 + - - +
464D GLN* 1.3 74.6 - - - +
466D VAL* 1.3 61.6 + - - +
468D ASP* 3.3 7.3 + - - +
469D ASP* 2.9 32.9 + - - +
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Residues in contact with VAL 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 4.2 6.0 - - + +
408D PHE* 4.1 25.6 - - + -
419D MET* 3.9 18.6 - - + -
420D PRO* 3.2 28.3 - - + +
421D VAL* 3.7 13.0 - - + -
431D LEU* 3.9 2.2 - - + -
462D SER 3.7 13.0 - - - +
463D PHE* 3.0 26.2 + - + +
465D MET* 1.3 75.0 - - - +
467D ILE* 1.3 56.3 + - - +
469D ASP* 3.1 6.5 + - - +
470D ILE* 2.9 37.8 + - + +
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Residues in contact with ILE 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 4.1 17.7 - - + -
25C HIS* 3.5 35.0 - - + +
463D PHE* 3.0 42.3 + - + +
464D GLN* 3.5 29.2 - - - +
466D VAL* 1.3 74.8 - - - +
468D ASP* 1.3 66.5 + - - +
470D ILE* 3.1 17.9 + - + +
471D PHE* 3.2 42.0 + - + -
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Residues in contact with ASP 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D ARG* 2.7 36.6 + - - -
464D GLN* 2.9 37.8 + - - +
465D MET 3.6 4.3 - - - +
467D ILE* 1.3 78.1 - - - +
469D ASP* 1.3 57.6 + - - +
471D PHE* 3.3 6.5 + - - +
472D ALA* 2.9 29.1 + - - +
480D GLY* 3.5 23.8 - - - +
481D ARG 4.8 4.1 - - - +
482D PRO* 5.0 2.0 - - - +
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Residues in contact with ASP 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 3.9 20.9 - - + +
293D TRP* 5.3 6.4 - - - -
421D VAL* 3.4 6.6 - - - +
422D ARG* 3.0 38.0 + - - +
453D ARG* 2.9 41.4 + - - -
465D MET 2.9 17.2 + - - +
466D VAL 3.1 4.9 + - - +
468D ASP* 1.3 72.4 - - - +
470D ILE* 1.3 66.2 + - - +
471D PHE 3.3 0.3 + - - -
472D ALA* 3.3 15.3 + - - +
473D VAL* 4.6 2.4 + - - +
478D LEU 4.8 2.5 - - - +
479D ILE 4.0 0.5 - - - -
480D GLY 2.9 13.3 + - - -
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Residues in contact with ILE 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 3.9 25.6 - - + -
22C ILE* 4.4 12.3 - - + -
800C CNC 4.0 25.0 - - + -
222D THR* 4.0 19.5 - - + -
223D LEU* 4.3 8.1 - - + -
293D TRP* 5.6 4.0 - - - -
296D GLY* 4.9 12.6 + - - +
408D PHE* 3.8 31.4 - - + -
463D PHE* 5.9 1.3 - - + -
466D VAL* 2.9 25.1 + - + +
467D ILE* 3.1 13.9 + - + +
469D ASP* 1.3 77.1 - - - +
471D PHE* 1.3 65.6 + - + +
472D ALA 3.8 0.2 + - - -
473D VAL* 5.0 1.7 + - - +
474D GLY 5.5 0.7 + - - -
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Residues in contact with PHE 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 3.8 23.3 - - + -
122C PRO* 6.4 0.4 - - + -
123C PRO* 5.1 6.5 - - + -
800C CNC 3.3 44.6 - - + -
467D ILE* 3.2 42.3 + - + +
468D ASP* 3.9 6.7 - - - +
469D ASP 3.2 0.6 - - - -
470D ILE* 1.3 80.7 - - + +
472D ALA* 1.3 66.0 + - - +
473D VAL 3.4 2.2 - - - -
474D GLY* 3.3 6.1 + - - -
475D LYS* 3.1 50.6 + - + +
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Residues in contact with ALA 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D ASP 2.9 16.3 + - - +
469D ASP 3.3 8.4 + - - +
471D PHE* 1.3 77.0 - - - +
473D VAL* 1.3 64.6 + - + +
475D LYS* 3.0 17.5 + - - +
476D GLY 3.0 8.8 + - - -
477D ARG* 2.9 24.1 + - + +
478D LEU 3.5 17.0 - - - +
479D ILE 3.8 3.8 - - - +
480D GLY* 3.7 17.0 - - - +
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Residues in contact with VAL 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B MET* 3.4 13.1 - - + +
353B MET* 3.8 18.6 - - + -
293D TRP* 3.5 43.3 - - + +
296D GLY 3.5 19.5 - - - +
298D PRO* 3.7 17.4 - - + +
307D VAL* 4.0 14.4 - - + -
469D ASP 4.6 2.5 + - - +
470D ILE 5.0 1.4 + - - +
471D PHE 3.4 0.4 - - - -
472D ALA* 1.3 75.9 - - + +
474D GLY* 1.3 61.7 + - - +
476D GLY* 3.0 10.4 + - - -
477D ARG 3.1 15.7 - - - +
478D LEU* 4.2 11.0 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il